Water impoundments have major impacts on biogeochemical cycles at the local and global scales. However, although reservoirs flood soils, their biogeochemical evolution below water and its ecological consequences are very poorly documented. We took advantage of the complete emptying of the Guerlédan Reservoir (Brittany, France) to compare the composition of soils flooded for 84 years with that of adjacent non-flooded soils used as reference, in 3 situations contrasted by their soil type (Cambisol and Podzol) and initial land-use (forest or grassland). In the annual drawdown zone, upper horizons of submerged soils are eroded, especially near the upper shore and on slopes. In the permanently drowned area, silty sediments cover drowned soils. Compared to reference soils, forest soils drowned for 84 years maintain their original morphological differentiation, but colors are dull, and the humus (O horizons) have virtually disappeared. Spodic horizons are depleted in poorly crystallized iron minerals while the accumulation of amorphous aluminum compounds remains unchanged. Soil bulk density increases as well as pH while total phosphorus content is almost unchanged. On the other hand, the pH of drowned grassland soils is lower by almost one unit, and the total phosphorus content was halved compared to reference soils. In this context, in addition to the effects of flooding, differences are attributed to post-1950 changes in agricultural practices i.e., liming and fertilization. Organic matter stocks decrease by almost 40%. This rate is similar in Cambisols and Podzols. Assuming that carbon was lost as CO2 and CH4, the corresponding flux averaged over the reservoir’s life is close to global areal estimates of CO2 emissions in temperate reservoirs and offsets a significant proportion of the carbon burial in reservoir sediments. Hence, flooded soils contribute significantly to the GHG budget of reservoirs, provide original long-term experimental sites to measure the effects of anoxia on soils and contain archives of past soil properties.